Severe acute respiratory syndrome (SARS) is a recently emerging disease associated with atypical pneumonia in infected patients. The disease is unusually severe, and there is no known treatment. The incubation period for. SARS is typically between 2 and 10 days. Sympathkumar et al., Mayo Clin. Proc. 78:882-890 (2003). Physical manifestations of SARS include fever, followed by a dry, nonproductive cough and shortness of breath. Death from respiratory failure occurs in about 3% to 10% of SARS cases. Centers for Disease Control and Prevention (CDC). Morb. Mortal. Wkly. Report. 52:357 (2003).
Clinical diagnosis of SARS is often a slow process because initial diagnostic testing of suspected SARS patients includes a chest radiograph, pulse oximetry, blood culture, sputum Gram's stain and culture, and testing for other viral respiratory infections. CDC, Guidelines and Recommendations: Interim Guidelines for Laboratory Diagnosis of SARS-CoV Infection, July (2003). This difficulty is also reflected by the fact that two of the most common diagnostic procedures—detection of serum antibodies to the SARS virus and isolation in cell culture of the virus from a clinical specimen—often take days or even weeks to complete. CDC, Guidelines and Recommendations: Interim Guidelines for Laboratory Diagnosis of SARS-CoV Infection, July (2003). Thus, the need for the establishment of a rapid and noninvasive test for SARS is essential for monitoring and control of the disease.
Early in 2003, a novel coronavirus was identified as the causative agent of SARS. Drosten et al., N. Engl. J. Med. 348:1967-76 (2003). The coronaviruses are a diverse group of RNA viruses that cause respiratory and enteric diseases in humans and other animals. They are the largest of the RNA viruses, with a genome of approximately 30,000 nucleotides. Rota et al., Science 300:1394-1399 (2003). The SARS-Coronavirus (SARS-CoV) is an enveloped, positive-stranded RNA virus. Based on sequence analysis, SARS-CoV is a member of a new group of coronavirus (order Nidovirales, Family Coronaviridae, genus Coronavirus). Rota et al., supra.
The replicase (rep) gene, is located towards the 5′ end of the genomic RNA and comprises approximately 70% of the whole genome. In contrast with other viral proteins, the rep gene products are translated from the genomic RNA. The replicase polyprotein undergo autocatalytic cleavage to yield functional viral proteases, RNA polymerase and RNA-dependent helicase. Detection of the rep gene may be used as an indicator of the presence of genomic SARS-CoV RNA. Rota et al., supra. An assay that tests for the presence of the viral nucleic acid would therefore allow for the rapid and sensitive detection of SARS-CoV. Such an assay would provide a more sensitive alternative to serological testing, direct fluorescent antibody staining or urinary antigen testing.